Solutions for Exercise 8

The RMS error for the overlay of the A RNA model onto tRNA(Phe) is 2.26 Å. The analogous overlay can be made by matching bases 6b-9b of the B RNA model onto nucleotides 34-36 of the tRNA molecule. For this model, the RMS error is 4.56 Å. Clearly, the conformation of the anticodon more closely matches the A conformation that the B conformation.

In looking at the possible stabilizing interactions between wybutosine and the base pairs of the codon-anticodon duplex, one has to take a significant leap of faith, since there is no assurance that the model we've prepared is accurate. However, observation of the complex shows that N20 of wybutosine is capable of forming an H-bond to O4 of Uridine 1A of the A RNA model. To see how this might work, you can look at the file combine.pdb using Midas.

In comparing the solvent accessible surface area of the UA base pair (see bp.fil), with wybutosine present, the total area is 67 sq. Å while with adenine it is 76 sq. Å.